Knowledge of the interactions occurring between specific proteins can provide important links to their functions. Attempts to develop an understanding of the interactions that occur on a genome wide scale for model organisms, yeast and nematodes, are ongoing. Similar information form mammalian systems is highly desirable. However, the approximately 10 fold greater complexity of the mammalian genome leads to an exponential increase in the difficulty of assessing all of the potential interactions. The present proposal will develop methodologies that enhance the efficiency with which techniques that have been successful in establishing genome wide protein interaction maps in model organisms can be applied to mammalian systems. The specific technique that will be modified here is the traditional yeast two-hybrid system. Once the methodologies are established, they will be sufficiently powerful to allow a complete protein interaction map to be established for all of the 1 x 10(10) potential interactions that are possible in a mammalian cell within less than 3 months using a single high throughput capillary sequencer. Based on the utility of similar protein interaction maps in model organisms, this work can be expected to provide an enormous wealth of insight into the function of mammalian cells.